The genome of the MZM-0403 strain of the African turquoise killifish, Nothobranchius furzeri.

Abstract

The African turquoise killifish, Nothobranchius furzeri, is an emerging model for functional genomics research. Interest in N. furzeri stems from its extremely short lifespan, and the breadth of research on this fish is rapidly expanding. All currently available whole-genome assemblies for N. furzeri are based on the GRZ strain. However, N. furzeri shows substantial phenotypic differences among populations. Here, we present a whole-genome assembly of the MZM-0403 strain of N. furzeri, which differs from the GRZ strain with respect to lifespan and male coloration patterns. We used PacBio HiFi sequencing to sequence the genome of an MZM-0403 male to ∼48 × coverage. The PacBio reads were de novo assembled and then scaffolded against an existing N. furzeri genome assembly. This strategy resulted in a chromosome-level assembly. Our MZM-0403 assembly differs from previous N. furzeri assemblies in that it is closer to the expected genome size based on independent estimates (∼1.5 Gb) and it has substantially fewer gaps, particularly in the vicinity of genes and within introns. A repeat analysis shows that about two-thirds of the genome is composed of repetitive elements. In addition, our assembly approach allowed us to recover phased fragments of the X- and Y-chromosomes. Analysis of these regions identifies 20 genes that are likely in the nonrecombining region of the sex chromosomes. Overall, this novel genome assembly will be useful for future functional and comparative genomics studies of fishes in the genus Nothobranchius.